Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012906.1 Kokia drynarioides strain JFW-HI SEQ_127920, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 90742
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 291 characters in sequence are not A, C, G, or T
Found at i:7095 original size:157 final size:158
Alignment explanation
Indices: 6804--7266 Score: 540
Period size: 157 Copynumber: 2.9 Consensus size: 158
6794 TTTTGGGTGT
* * *
6804 TGGTCTTGGATGTCTTACCGATGGCTAAGATCTTGCAATTGTTACAGATTCTCCA-AGCTCGTAT
1 TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT
* * * * * *
6868 GAGCAGCATCGTGTAGCTTAACATCTCGACTCAAAACTCGTGTGAGTAGGCCTATTTCACAGATC
66 GAGTAGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGATC
* * * * *
6933 GTGTGAGTCGTACAGGATAT-AGAGTGC
131 ATGTGAGCCATACAAGATATAAGAGTAC
** * *
6960 TGGTCTTAAATGTCCTACCGATGGCTGAGGTCTTGCAATTATTACAGATTCTCCACAGCTCGTGT
1 TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT
* * * *
7025 GAGTAACATCGTGTAGCTTAAGATCCCGACCCATAGCTCGTGTGAGTAGGCCGATTTCACTGATC
66 GAGTAGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGATC
*
7090 ATGTGAGCCATACAAGATATAAGGGTAC
131 ATGTGAGCCATACAAGATATAAGAGTAC
** * * * * * *
7118 T-GAATTGGATGTCCTACCGATAGTTGAGATTTTGCAATTGTTGCTGATTCTCCACAGGTCGTGT
1 TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT
* ** *
7182 GA-TCAGCATCGTGTAGCTTAACATCCCGACCCATAGCTTGTGTGAACAGGCCCATTTCACAGCT
66 GAGT-AGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGAT
* *
7246 CGTGTAAG-CATTACAAGATAT
130 CATGTGAGCCA-TACAAGATAT
7267 GGATATTTTA
Statistics
Matches: 259, Mismatches: 44, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
156 52 0.20
157 201 0.78
158 6 0.02
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (158 bp):
TGGTCTTGGATGTCCTACCGATGGCTGAGATCTTGCAATTGTTACAGATTCTCCACAGCTCGTGT
GAGTAGCATCGTGTAGCTTAACATCCCGACCCATAGCTCGTGTGAGTAGGCCCATTTCACAGATC
ATGTGAGCCATACAAGATATAAGAGTAC
Found at i:9391 original size:41 final size:41
Alignment explanation
Indices: 9266--9396 Score: 174
Period size: 41 Copynumber: 3.2 Consensus size: 41
9256 ACAGAAAACG
* *
9266 CCGCAAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCG
1 CCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCA
* * *
9307 CCGCTAAAAGTCAAAGCAATAGCGACGCTTATGGAAAAACA
1 CCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCA
* * *
9348 CCGCTAAAGGTCAGAGCAATAGCGACACTTACAGG-CAAGCA
1 CCGCTAAAGGTCAGAGCAATAGCGACGCTTA-TGGAAAAGCA
9389 CCGCTAAA
1 CCGCTAAA
9397 AATCAGTGCA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 76 0.97
42 2 0.03
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (41 bp):
CCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGAAAAGCA
Found at i:9425 original size:24 final size:24
Alignment explanation
Indices: 9389--9443 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
9379 CAGGCAAGCA
9389 CCGCTAAAAATCAG-TGCATTAGCG
1 CCGCTAAAAATCAGAT-CATTAGCG
*
9413 CCGCTAAAGATCAGATCATTAGCG
1 CCGCTAAAAATCAGATCATTAGCG
*
9437 ACGCTAA
1 CCGCTAA
9444 TTGGAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (24 bp):
CCGCTAAAAATCAGATCATTAGCG
Found at i:9564 original size:19 final size:19
Alignment explanation
Indices: 9542--9584 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
9532 TTATATAAAC
*
9542 TAAAAAAATTCTAAAATTT
1 TAAAAAAATTATAAAATTT
* *
9561 TAAAAAATTTATTAAATTT
1 TAAAAAAATTATAAAATTT
9580 TAAAA
1 TAAAA
9585 CTTATATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAAAATTATAAAATTT
Found at i:11252 original size:23 final size:22
Alignment explanation
Indices: 11210--11254 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11200 GTTTTCCTGC
*
11210 CTTTTTAGTATGTGCTTTCTTT
1 CTTTTTAGTATGTGCATTCTTT
*
11232 CTTTTTAGTATGTTCAATTCTTT
1 CTTTTTAGTATGTGC-ATTCTTT
11255 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.62
Consensus pattern (22 bp):
CTTTTTAGTATGTGCATTCTTT
Found at i:13592 original size:21 final size:21
Alignment explanation
Indices: 13568--13607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13558 GGCGTTTGTG
*
13568 GGGAAAGTGTCGTTAAAGAAC
1 GGGAAAGCGTCGTTAAAGAAC
*
13589 GGGAAAGCGTTGTTAAAGA
1 GGGAAAGCGTCGTTAAAGA
13608 CCATGTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGAAAGCGTCGTTAAAGAAC
Found at i:13698 original size:42 final size:42
Alignment explanation
Indices: 13589--13701 Score: 136
Period size: 43 Copynumber: 2.7 Consensus size: 42
13579 GTTAAAGAAC
* *
13589 GGGAAAGCGTTGTTAAAGACCATGTTATTTAACGGTGTTTAT
1 GGGAAAGCGTTGTTAAAGACCATGTTCTTTAACGGTGTTCAT
** * * *
13631 GGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGTGTTCGT
1 GGG-AAAGCGTTGTTAAAGACCATGTTCTTTAACGGTGTTCAT
* *
13674 GGGAAAGCGTTGTTAAATATCATGTTCT
1 GGGAAAGCGTTGTTAAAGACCATGTTCT
13702 ATAGTGGCGT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 23 0.40
43 35 0.60
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (42 bp):
GGGAAAGCGTTGTTAAAGACCATGTTCTTTAACGGTGTTCAT
Found at i:18120 original size:96 final size:96
Alignment explanation
Indices: 17954--18127 Score: 228
Period size: 96 Copynumber: 1.8 Consensus size: 96
17944 TCAATTATCC
* ** * * * *
17954 CGATTTGATGAAAGGTTGCACCTAGTAAGTTAGGGCGTAAATTTTTAGAATCGAAGATAAGGAAA
1 CGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCGAAGATAAAGAAA
18019 CATTGCCTCGATTAAGGGTATTCGATTATTT
66 CATTGCCTCGATTAAGGGTATTCGATTATTT
18050 CGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCGA-AACTCGAA-ATAAA-A
1 CGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-GAGAA-TCGAAGATAAAGA
*
18112 GAATATTGCCTCGATT
64 -AACATTGCCTCGATT
18128 TTAAAGTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 60 0.90
97 6 0.09
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
CGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAGAATCGAAGATAAAGAAA
CATTGCCTCGATTAAGGGTATTCGATTATTT
Found at i:18372 original size:29 final size:28
Alignment explanation
Indices: 18340--18402 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
18330 AAAATGAGAC
* **
18340 TTTTCGGATACCCGGGGGTAAAATGGTAA
1 TTTT-GGATACCCGAGGCAAAAATGGTAA
* *
18369 TTTTGGATTCTCGAGGCAAAAATGGTAA
1 TTTTGGATACCCGAGGCAAAAATGGTAA
18397 TTTTGG
1 TTTTGG
18403 GAAAATTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTGGATACCCGAGGCAAAAATGGTAA
Found at i:18568 original size:29 final size:29
Alignment explanation
Indices: 18535--18695 Score: 175
Period size: 29 Copynumber: 5.5 Consensus size: 29
18525 TTTGGGGTCA
18535 AAAATGGGATTTTTGGAAGTTCGGGAGTT
1 AAAATGGGATTTTTGGAAGTTCGGGAGTT
** *
18564 AAAATGGGATTTTTGGAAGTT-TTGATGTCA
1 AAAATGGGATTTTTGGAAGTTCGGGA-GT-T
* *
18594 AAAATGGGATTTTTGGAAGTTCGAGAGTA
1 AAAATGGGATTTTTGGAAGTTCGGGAGTT
* *
18623 AAAATAGGATTTTTGGAAGTTTTGGG-GTT
1 AAAATGGGATTTTTGGAAG-TTCGGGAGTT
* *
18652 AAAAATGGGATTTTTTGAAGTTTTGGG-GTT
1 -AAAATGGGATTTTTGGAAG-TTCGGGAGTT
18682 AAAATGGGATTTTT
1 AAAATGGGATTTTT
18696 TTGAAGTTTT
Statistics
Matches: 116, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
28 2 0.02
29 58 0.50
30 54 0.47
31 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.39
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTCGGGAGTT
Found at i:18580 original size:59 final size:59
Alignment explanation
Indices: 18506--18734 Score: 307
Period size: 59 Copynumber: 3.8 Consensus size: 59
18496 TTAGGGGCAT
* *
18506 AAATGGAAGTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGAGTTA
1 AAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGAGTTA
** * *
18565 AAATGGGATTTTTGGAAGTTTTGATGTCAAAAATGGGATTTTTGGAAGTTCGAGAGTAA
1 AAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGAGTTA
* * * *
18624 AAATAGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTTGAAGTTTTGGG-GTTA
1 AAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGAGTTA
* * *
18683 AAATGGGATTTTTTTGAAGTTTTGGGATCAAAAATGGAATTTTTGGATAGTT
1 AAATGGGA-TTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGA-AGTT
18735 TAGGGATCCT
Statistics
Matches: 147, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
59 106 0.72
60 39 0.27
61 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.38
Consensus pattern (59 bp):
AAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGAGTTA
Found at i:18696 original size:29 final size:29
Alignment explanation
Indices: 18472--18735 Score: 266
Period size: 30 Copynumber: 8.9 Consensus size: 29
18462 AGAGTTTCGA
*
18472 GGGTAAAAAT-GGA-ATTTGGAAGTTTTAG
1 GGGTAAAAATGGGATTTTTGGAAGTTTT-G
* * * *
18500 GGGCATAAATGGAAGTTTTGGAAGTTTTG
1 GGGTAAAAATGGGATTTTTGGAAGTTTTG
*
18529 GGGTCAAAAATGGGATTTTTGGAAG-TTCG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTTG
*
18558 GGAGTTAAAATGGGATTTTTGGAAGTTTTG
1 GG-GTAAAAATGGGATTTTTGGAAGTTTTG
** *
18588 ATGTCAAAAATGGGATTTTTGGAAG-TTCG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTTG
* *
18617 AGAGTAAAAATAGGATTTTTGGAAGTTTTG
1 -GGGTAAAAATGGGATTTTTGGAAGTTTTG
*
18647 GGGTTAAAAATGGGATTTTTTGAAGTTTTG
1 GGG-TAAAAATGGGATTTTTGGAAGTTTTG
* *
18677 GGGTTAAAATGGGATTTTTTTGAAGTTTTG
1 GGGTAAAAATGGGA-TTTTTGGAAGTTTTG
* *
18707 GGATCAAAAATGGAATTTTTGGATAGTTT
1 GGGT-AAAAATGGGATTTTTGGA-AGTTT
18736 AGGGATCCTC
Statistics
Matches: 197, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.04
29 66 0.34
30 110 0.56
31 13 0.07
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.38
Consensus pattern (29 bp):
GGGTAAAAATGGGATTTTTGGAAGTTTTG
Found at i:19770 original size:3 final size:3
Alignment explanation
Indices: 19682--19755 Score: 67
Period size: 3 Copynumber: 23.0 Consensus size: 3
19672 TTCGATTTTT
* * * *
19682 TTA TTA TTAA TTA TTA ATA TTA CTA TTA TTA TTA TTAA TGA TGCA GTTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T-TA -TTA
19731 TTA CTTA TTA TTA TTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA
19756 GCACATTTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
3 48 0.81
4 10 0.17
5 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:20511 original size:45 final size:45
Alignment explanation
Indices: 20462--20550 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
20452 GTTTGTGTTA
* *
20462 GGTGTAATTGGGTCATTGGGCTAGTCTTTGGGCCCTTTGTAATTG
1 GGTGTAATTGGGCCATTGGGCTAGTCTTTAGGCCCTTTGTAATTG
20507 GGTGTAATTGGGCCATTGGGCTAGTCTTTAGGCCCTTTGTAATT
1 GGTGTAATTGGGCCATTGGGCTAGTCTTTAGGCCCTTTGTAATT
20551 AGGACATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.39
Consensus pattern (45 bp):
GGTGTAATTGGGCCATTGGGCTAGTCTTTAGGCCCTTTGTAATTG
Found at i:20612 original size:17 final size:17
Alignment explanation
Indices: 20571--20641 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
20561 TAATGAACTT
*
20571 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAAATT-AA
* *
20589 ATTAAATTTAAGATTAA
1 TTTAAATTTAAAATTAA
*
20606 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATTAA
* *
20623 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATTAA
20640 TT
1 TT
20642 AAAAAATGGC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:24647 original size:16 final size:15
Alignment explanation
Indices: 24599--24638 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
24589 ATGTGAAGAT
*
24599 CAAAATTTTTAAAAA
1 CAAAATTGTTAAAAA
*
24614 AAAAATTGTTAAAAA
1 CAAAATTGTTAAAAA
24629 CAAAATTGTT
1 CAAAATTGTT
24639 TAATCACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (15 bp):
CAAAATTGTTAAAAA
Found at i:24714 original size:12 final size:13
Alignment explanation
Indices: 24695--24720 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24685 AGAGACTTCA
24695 ATTTTTTTAAAAT
1 ATTTTTTTAAAAT
24708 ATTTTTTTAAAAT
1 ATTTTTTTAAAAT
24721 TATAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTTTTAAAAT
Found at i:27223 original size:22 final size:23
Alignment explanation
Indices: 27198--27244 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 23
27188 CATTTGACTT
27198 AACACACAAGAGTATATC-AAAC
1 AACACACAAGAGTATATCAAAAC
* *
27220 -A-ACATAAGAGTGTATCAAAAC
1 AACACACAAGAGTATATCAAAAC
27241 AACA
1 AACA
27245 TTCATCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
20 13 0.65
21 5 0.25
22 1 0.05
23 1 0.05
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (23 bp):
AACACACAAGAGTATATCAAAAC
Found at i:27230 original size:20 final size:21
Alignment explanation
Indices: 27205--27245 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
27195 CTTAACACAC
27205 AAGAGTATATC-AAACAACAT
1 AAGAGTATATCAAAACAACAT
*
27225 AAGAGTGTATCAAAACAACAT
1 AAGAGTATATCAAAACAACAT
27246 TCATCCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGAGTATATCAAAACAACAT
Found at i:27639 original size:27 final size:28
Alignment explanation
Indices: 27589--27653 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
27579 AAAAACGGCT
*
27589 TATTCGAGCCAAACACAAAATAATGTTC
1 TATTCGAGCCAAACACAAAATAATGCTC
* * *
27617 T-TTCGAGCCAAATACAGAGTAATGCTC
1 TATTCGAGCCAAACACAAAATAATGCTC
27644 TATT-GAGCCA
1 TATTCGAGCCA
27654 GAGCTCAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (28 bp):
TATTCGAGCCAAACACAAAATAATGCTC
Found at i:27670 original size:28 final size:27
Alignment explanation
Indices: 27639--27777 Score: 129
Period size: 28 Copynumber: 5.0 Consensus size: 27
27629 TACAGAGTAA
*
27639 TGCTCTATTGAGCCAGAGCTCAGAATAT
1 TGCTCT-TTGAGCCAGAGTTCAGAATAT
* * * *
27667 TGCTCTTTCAAGCCAAAGTTCAGAGTAA
1 TGCTCTTT-GAGCCAGAGTTCAGAATAT
* *
27695 TGCTTTATTGAGCCAGA-TACA-AATAT
1 TGCTCT-TTGAGCCAGAGTTCAGAATAT
* *
27721 TACTCTTTCGAGCCAGAATTCAGAATAT
1 TGCTCTTT-GAGCCAGAGTTCAGAATAT
*
27749 TGCTCTTTTGAGCCGGAGTTCAGAATAT
1 TGCTC-TTTGAGCCAGAGTTCAGAATAT
27777 T
1 T
27778 ATTTAAATAT
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
25 2 0.02
26 15 0.17
27 8 0.09
28 58 0.66
29 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (27 bp):
TGCTCTTTGAGCCAGAGTTCAGAATAT
Found at i:27737 original size:26 final size:28
Alignment explanation
Indices: 27615--27778 Score: 90
Period size: 28 Copynumber: 6.0 Consensus size: 28
27605 AAAATAATGT
* * *
27615 TCTTTCGAGCCA-AATACAGAGTAATGC
1 TCTTTCGAGCCAGAATACAGAATATTAC
* *
27642 TCTATT-GAGCCAGAGCT-CAGAATATTGC
1 TCT-TTCGAGCCAGA-ATACAGAATATTAC
* * * * *
27670 TCTTTCAAGCCA-AAGTTCAGAGTAATGC
1 TCTTTCGAGCCAGAA-TACAGAATATTAC
*
27698 T-TTATTGAGCCAG-ATACA-AATATTAC
1 TCTT-TCGAGCCAGAATACAGAATATTAC
* *
27724 TCTTTCGAGCCAGAATTCAGAATATTGC
1 TCTTTCGAGCCAGAATACAGAATATTAC
* * * *
27752 TCTTTTGAGCCGGAGTTCAGAATATTA
1 TCTTTCGAGCCAGAATACAGAATATTA
27779 TTTAAATATT
Statistics
Matches: 106, Mismatches: 20, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
26 14 0.13
27 24 0.23
28 67 0.63
29 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (28 bp):
TCTTTCGAGCCAGAATACAGAATATTAC
Found at i:27744 original size:54 final size:54
Alignment explanation
Indices: 27615--27778 Score: 181
Period size: 54 Copynumber: 3.0 Consensus size: 54
27605 AAAATAATGT
* * *
27615 TCTTTCGAGCCAAATACAGAGTAATGCTCTATTGAGCCAGAGCTCAGAATATTGC
1 TCTTTCGAGCCAAATTCAGAGTAATGCTTTATTGAGCCAGA-CTCAGAATATTAC
*
27670 TCTTTCAAGCCAAAGTTCAGAGTAATGCTTTATTGAGCCAGA-TACA-AATATTAC
1 TCTTTCGAGCCAAA-TTCAGAGTAATGCTTTATTGAGCCAGACT-CAGAATATTAC
* * * *
27724 TCTTTCGAGCCAGAATTCAGAATATTGCTCTT-TTGAGCCGGAGTTCAGAATATTA
1 TCTTTCGAGCCA-AATTCAGAGTAATGCT-TTATTGAGCCAGA-CTCAGAATATTA
27779 TTTAAATATT
Statistics
Matches: 94, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
54 40 0.43
55 21 0.22
56 33 0.35
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (54 bp):
TCTTTCGAGCCAAATTCAGAGTAATGCTTTATTGAGCCAGACTCAGAATATTAC
Found at i:40438 original size:12 final size:12
Alignment explanation
Indices: 40418--40449 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40408 AAAACATAAA
40418 TTTTATTATTTT
1 TTTTATTATTTT
*
40430 TTTTGTTATTTT
1 TTTTATTATTTT
40442 TTTTATTA
1 TTTTATTA
40450 ATCATTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (12 bp):
TTTTATTATTTT
Found at i:43757 original size:21 final size:21
Alignment explanation
Indices: 43733--43775 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
43723 AAATTAGGGC
43733 ACAACATCCCGAATCTTCGAA
1 ACAACATCCCGAATCTTCGAA
*
43754 ACAACATCTCGAATCTTCGAA
1 ACAACATCCCGAATCTTCGAA
43775 A
1 A
43776 ATAAAGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (21 bp):
ACAACATCCCGAATCTTCGAA
Found at i:44379 original size:14 final size:14
Alignment explanation
Indices: 44362--44406 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
44352 AGTAAGCATA
44362 AAAAATAAATAAAG
1 AAAAATAAATAAAG
*
44376 AAAAATAAATAAAT
1 AAAAATAAATAAAG
44390 AAAATATAAAATAAAG
1 AAAA-AT-AAATAAAG
44406 A
1 A
44407 GCTGCATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 17 0.63
15 2 0.07
16 8 0.30
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (14 bp):
AAAAATAAATAAAG
Found at i:44383 original size:21 final size:21
Alignment explanation
Indices: 44341--44392 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
44331 TAAATGGGAT
**
44341 AAAAATAAATAAGTAAGCATA
1 AAAAATAAATAAGTAAAAATA
44362 AAAAATAAATAAAG-AAAAATA
1 AAAAATAAAT-AAGTAAAAATA
44383 AATAAATAAA
1 AA-AAATAAA
44393 ATATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAAATAAATAAGTAAAAATA
Found at i:51561 original size:12 final size:12
Alignment explanation
Indices: 51519--51614 Score: 67
Period size: 12 Copynumber: 8.3 Consensus size: 12
51509 ATAACATCCA
51519 AACAACAAAAAT
1 AACAACAAAAAT
51531 AACAATC-AAAAT
1 AACAA-CAAAAAT
** *
51543 AGTAGCAAAAAT
1 AACAACAAAAAT
*
51555 AACAGC---AA-
1 AACAACAAAAAT
*
51563 AACAACTAAAAT
1 AACAACAAAAAT
*
51575 AGCAACAAAAAT
1 AACAACAAAAAT
* *
51587 AACAGCAAAAAC
1 AACAACAAAAAT
*
51599 AGCAACAAAAAT
1 AACAACAAAAAT
51611 AACA
1 AACA
51615 TCATTTGTCG
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
11 3 0.05
12 52 0.83
13 1 0.02
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:51586 original size:44 final size:44
Alignment explanation
Indices: 51506--51597 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
51496 AAAATGCATG
* * **
51506 AAAATAACATCCAAACAACAAAAATAACAATCAAAATAGTAGCA
1 AAAATAACAGCAAAACAACAAAAATAACAATCAAAATAACAGCA
* *
51550 AAAATAACAGCAAAACAACTAAAATAGCAA-CAAAAATAACAGCA
1 AAAATAACAGCAAAACAACAAAAATAACAATC-AAAATAACAGCA
51594 AAAA
1 AAAA
51598 CAGCAACAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.66, C:0.17, G:0.05, T:0.11
Consensus pattern (44 bp):
AAAATAACAGCAAAACAACAAAAATAACAATCAAAATAACAGCA
Found at i:51608 original size:44 final size:44
Alignment explanation
Indices: 51518--51608 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
51508 AATAACATCC
** * *
51518 AAACAACAAAAATAACAATCAAAATAGTAGCAAAAATAACAGCA
1 AAACAACAAAAATAACAATCAAAATAACAGCAAAAACAACAACA
* * *
51562 AAACAACTAAAATAGCAA-CAAAAATAACAGCAAAAACAGCAACA
1 AAACAACAAAAATAACAATC-AAAATAACAGCAAAAACAACAACA
51606 AAA
1 AAA
51609 ATAACATCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.03
44 38 0.97
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (44 bp):
AAACAACAAAAATAACAATCAAAATAACAGCAAAAACAACAACA
Found at i:52556 original size:30 final size:30
Alignment explanation
Indices: 52477--52672 Score: 159
Period size: 30 Copynumber: 6.6 Consensus size: 30
52467 TGGGAAAAAT
** * * *
52477 GGGGTCAAAAATGAAATTTTAGAGAATTTTA
1 GGGGTC-AAAATGTGATTTTGGAAAAGTTTA
* * * *
52508 AGGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTCAAAATGTGATTTTGGAAAAGTTTA
* *
52538 GGGGTTAAAATGTGATTTTGG-GAAGTTTA
1 GGGGTCAAAATGTGATTTTGGAAAAGTTTA
* * *
52567 GAGGTCAAAATGTGATTTTGGGAAAGTTAA
1 GGGGTCAAAATGTGATTTTGGAAAAGTTTA
* *
52597 GGGGTTAAAATGTGATTTTGGGAAA-TTT-
1 GGGGTCAAAATGTGATTTTGGAAAAGTTTA
* **
52625 GAGGATCAAAATGTGATTTAAGAAAA-TTT-
1 G-GGGTCAAAATGTGATTTTGGAAAAGTTTA
*
52654 GCGGTCAAAATGTGATTTT
1 GGGGTCAAAATGTGATTTT
52673 TGGGTAAAAT
Statistics
Matches: 137, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.12
29 51 0.37
30 66 0.48
31 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (30 bp):
GGGGTCAAAATGTGATTTTGGAAAAGTTTA
Found at i:52586 original size:59 final size:59
Alignment explanation
Indices: 52522--52672 Score: 209
Period size: 59 Copynumber: 2.6 Consensus size: 59
52512 TTAAAATATA
*
52522 ATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTGGGAAGTTTAGAGG-TCAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTGGGAAATTT-GAGGATCAAAATGTG
* *
52581 ATTTTGGGAAAGTTAAGGGGTTAAAATGTGATTTTGGGAAATTTGAGGATCAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTGGGAAATTTGAGGATCAAAATGTG
** * *
52640 ATTTAAGAAAA-TTT-GCGGTCAAAATGTGATTTT
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTT
52673 TGGGTAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
57 17 0.21
58 6 0.07
59 59 0.72
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (59 bp):
ATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTGGGAAATTTGAGGATCAAAATGTG
Found at i:52651 original size:29 final size:28
Alignment explanation
Indices: 52544--52671 Score: 94
Period size: 29 Copynumber: 4.4 Consensus size: 28
52534 TTTAGGGGTT
** * *
52544 AAAATGTGATTTTGGGAAGTTTAGAGGTC
1 AAAATGTGATTTAAGAAAATTT-GAGGTC
** * * * *
52573 AAAATGTGATTTTGGGAAAGTTAAGGGGTT
1 AAAATGTGA-TTTAAGAAAATT-TGAGGTC
** *
52603 AAAATGTGATTTTGGGAAATTTGAGGATC
1 AAAATGTGATTTAAGAAAATTTGAGG-TC
*
52632 AAAATGTGATTTAAGAAAATTTGCGGTC
1 AAAATGTGATTTAAGAAAATTTGAGGTC
52660 AAAATGTGATTT
1 AAAATGTGATTT
52672 TTGGGTAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
28 17 0.21
29 41 0.51
30 23 0.28
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAATGTGATTTAAGAAAATTTGAGGTC
Found at i:52662 original size:28 final size:29
Alignment explanation
Indices: 52603--52671 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
52593 TTAAGGGGTT
** *
52603 AAAATGTGATTTTGGGAAATTTGAGGATC
1 AAAATGTGATTTAAGAAAATTTGAGGATC
*
52632 AAAATGTGATTTAAGAAAATTTGCGG-TC
1 AAAATGTGATTTAAGAAAATTTGAGGATC
52660 AAAATGTGATTT
1 AAAATGTGATTT
52672 TTGGGTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGTGATTTAAGAAAATTTGAGGATC
Found at i:53358 original size:11 final size:11
Alignment explanation
Indices: 53342--53367 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53332 AAGTTTTGAT
53342 TTTTTCTTTTC
1 TTTTTCTTTTC
53353 TTTTTCTTTTC
1 TTTTTCTTTTC
53364 TTTT
1 TTTT
53368 CAAACCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:54286 original size:20 final size:21
Alignment explanation
Indices: 54252--54340 Score: 121
Period size: 21 Copynumber: 4.3 Consensus size: 21
54242 CTAACAGCAT
54252 CAAAACAGT-AAAAA-AACAC
1 CAAAACAGTAAAAAACAACAC
*
54271 CAAAACAGTAAAAAA-AACTC
1 CAAAACAGTAAAAAACAACAC
54291 CAAAACAGTAAAAAAACAACAC
1 CAAAACAGT-AAAAAACAACAC
* *
54313 CAAAAAAGTAAAAAACAGCAC
1 CAAAACAGTAAAAAACAACAC
54334 CAAAACA
1 CAAAACA
54341 ACAATATAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 9 0.15
20 18 0.29
21 23 0.37
22 12 0.19
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (21 bp):
CAAAACAGTAAAAAACAACAC
Found at i:54773 original size:31 final size:31
Alignment explanation
Indices: 54735--54799 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
54725 CTAGTTCGAT
*
54735 TGTATCTTTCCATTTTGATCAATCTAATCTA
1 TGTATCTTTCCATTTTGACCAATCTAATCTA
*
54766 TGTATCTTTCCATTTTGGCCAATCTAATCTA
1 TGTATCTTTCCATTTTGACCAATCTAATCTA
54797 TGT
1 TGT
54800 CAAGGTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (31 bp):
TGTATCTTTCCATTTTGACCAATCTAATCTA
Found at i:56109 original size:14 final size:14
Alignment explanation
Indices: 56090--56160 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
56080 TTCATTTATC
*
56090 ATCCTTTTGGATAT
1 ATCCTTTTGAATAT
*
56104 ATCCTTTTCAAATAT
1 ATCCTTTT-GAATAT
** *
56119 ATCAATTCGAATAT
1 ATCCTTTTGAATAT
* *
56133 AACCTTTTCAA-AT
1 ATCCTTTTGAATAT
*
56146 ATCCTTTTGGATAT
1 ATCCTTTTGAATAT
56160 A
1 A
56161 ATTTTTTCAA
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
13 10 0.24
14 22 0.54
15 9 0.22
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (14 bp):
ATCCTTTTGAATAT
Found at i:56120 original size:15 final size:15
Alignment explanation
Indices: 56100--56147 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
56090 ATCCTTTTGG
56100 ATATATCCTTTTCAA
1 ATATATCCTTTTCAA
** *
56115 ATATAT-CAATTCGA
1 ATATATCCTTTTCAA
*
56129 ATATAACCTTTTCAA
1 ATATATCCTTTTCAA
56144 ATAT
1 ATAT
56148 CCTTTTGGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (15 bp):
ATATATCCTTTTCAA
Found at i:56181 original size:27 final size:29
Alignment explanation
Indices: 56151--56209 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
56141 CAAATATCCT
56151 TTTGGAT-ATA-ATTTTTTCAATGATATC
1 TTTGGATGATATATTTTTTCAATGATATC
* * *
56178 TTT-GATGATATTTTTTTTCATTGATATT
1 TTTGGATGATATATTTTTTCAATGATATC
56206 TTTG
1 TTTG
56210 CGGATATCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 3 0.12
27 6 0.23
28 17 0.65
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (29 bp):
TTTGGATGATATATTTTTTCAATGATATC
Found at i:56194 original size:28 final size:28
Alignment explanation
Indices: 56164--56375 Score: 183
Period size: 28 Copynumber: 7.6 Consensus size: 28
56154 GGATATAATT
* ** *
56164 TTTTCAATGATATCTTTGATGATATTTT
1 TTTTCAATGATATCCTTGCGGATATTTC
* ** **
56192 TTTTCATTGATATTTTTGCGGATATCCC
1 TTTTCAATGATATCCTTGCGGATATTTC
*
56220 TTTTCAATAATATCCTTGCGGATATTT-
1 TTTTCAATGATATCCTTGCGGATATTTC
** **
56247 TTTTCTTTGATATCCTTGCGGATACCTC
1 TTTTCAATGATATCCTTGCGGATATTTC
* **
56275 TTTTCAATAATATCCTTGTAGATATTTC
1 TTTTCAATGATATCCTTGCGGATATTTC
* * **
56303 TTTTCATTGATATCCTTGCAGATATCCC
1 TTTTCAATGATATCCTTGCGGATATTTC
* * **
56331 TTTTCATTGATATTCTTGCGGATATCCC
1 TTTTCAATGATATCCTTGCGGATATTTC
*
56359 TTTTCAATAATATCCTT
1 TTTTCAATGATATCCTT
56376 ACGAATAAAA
Statistics
Matches: 148, Mismatches: 35, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
27 22 0.15
28 126 0.85
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTTCAATGATATCCTTGCGGATATTTC
Found at i:56355 original size:56 final size:56
Alignment explanation
Indices: 56164--56375 Score: 239
Period size: 56 Copynumber: 3.8 Consensus size: 56
56154 GGATATAATT
* * ** * **
56164 TTTTCAATGATATCTTTGATGATATTTTTTTTCATTGATATTTTTGCGGATATCCC
1 TTTTCAATAATATCCTTGCGGATATTTCTTTTCATTGATATCCTTGCGGATATCCC
*
56220 TTTTCAATAATATCCTTGCGGATATTT-TTTTCTTTGATATCCTTGCGGATA-CCTC
1 TTTTCAATAATATCCTTGCGGATATTTCTTTTCATTGATATCCTTGCGGATATCC-C
** *
56275 TTTTCAATAATATCCTTGTAGATATTTCTTTTCATTGATATCCTTGCAGATATCCC
1 TTTTCAATAATATCCTTGCGGATATTTCTTTTCATTGATATCCTTGCGGATATCCC
* * * ** * *
56331 TTTTCATTGATATTCTTGCGGATATCCCTTTTCAATAATATCCTT
1 TTTTCAATAATATCCTTGCGGATATTTCTTTTCATTGATATCCTT
56376 ACGAATAAAA
Statistics
Matches: 133, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
54 2 0.02
55 47 0.35
56 82 0.62
57 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (56 bp):
TTTTCAATAATATCCTTGCGGATATTTCTTTTCATTGATATCCTTGCGGATATCCC
Found at i:56363 original size:84 final size:83
Alignment explanation
Indices: 56219--56375 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 83
56209 GCGGATATCC
* ** *
56219 CTTTTCAATAATATCCTTGCGGATATTTTTTTCTTTGATATCCTTGCGGATACCTCTTTTCAATA
1 CTTTTCAATAATATCCTTGCAGATATCCTTTTCATTGATATCCTTGCGGATACCTCTTTTCAATA
56284 ATATCCTTGTAGATATTT
66 ATATCCTTGTAGATATTT
* * *
56302 CTTTTCATTGATATCCTTGCAGATATCCCTTTTCATTGATATTCTTGCGGATATCC-CTTTTCAA
1 CTTTTCAATAATATCCTTGCAGATAT-CCTTTTCATTGATATCCTTGCGGATA-CCTCTTTTCAA
56366 TAATATCCTT
64 TAATATCCTT
56376 ACGAATAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 23 0.35
84 40 0.62
85 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.47
Consensus pattern (83 bp):
CTTTTCAATAATATCCTTGCAGATATCCTTTTCATTGATATCCTTGCGGATACCTCTTTTCAATA
ATATCCTTGTAGATATTT
Found at i:56895 original size:21 final size:20
Alignment explanation
Indices: 56857--56895 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
56847 TTTCATATTT
* *
56857 TCAAAATCTAACACTTTCTA
1 TCAAAATCAAACAATTTCTA
56877 TCAAAACTCAAACAATTTC
1 TCAAAA-TCAAACAATTTC
56896 ACTCTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (20 bp):
TCAAAATCAAACAATTTCTA
Found at i:61797 original size:2 final size:2
Alignment explanation
Indices: 61790--61815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61780 NNNNNNNNNN
61790 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
61816 GTTTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:68135 original size:33 final size:33
Alignment explanation
Indices: 68081--68337 Score: 157
Period size: 33 Copynumber: 7.8 Consensus size: 33
68071 CCAACCCACG
* * * *
68081 CAGCCAAGTGCTAATCTATATGGCCAGCTTGCT
1 CAGCCAAGTGCTAACCCATATGGCCAGCATGGT
* * ** *
68114 CAGCCTAGTGCTAACCCATATGACCAAAATGGG
1 CAGCCAAGTGCTAACCCATATGGCCAGCATGGT
* * * * *
68147 CAACCAAGTGGTAATCCTTATGGCCAGCCT-GT
1 CAGCCAAGTGCTAACCCATATGGCCAGCATGGT
* ** *
68179 GCAGCCCAGTGCTAACCCATATGGCCAAAATGGG
1 -CAGCCAAGTGCTAACCCATATGGCCAGCATGGT
*
68213 CA-CTCAAGTGCTAATCCC-TATGGCCAGCCT-GT
1 CAGC-CAAGTGCTAA-CCCATATGGCCAGCATGGT
* * ** * *
68245 GCAGCCCAGTGCTAACCCATACGGCCAAAACGGG
1 -CAGCCAAGTGCTAACCCATATGGCCAGCATGGT
* *
68279 CAGCCAAGTGCTAATCCC-TATGGCCTGCCTGCGT
1 CAGCCAAGTGCTAA-CCCATATGGCCAGCATG-GT
* *
68313 CA-CCCAGTGCTAACTCATATGGCCA
1 CAGCCAAGTGCTAACCCATATGGCCA
68338 AAACGAGCAG
Statistics
Matches: 162, Mismatches: 51, Indels: 22
0.69 0.22 0.09
Matches are distributed among these distances:
32 8 0.05
33 142 0.88
34 12 0.07
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (33 bp):
CAGCCAAGTGCTAACCCATATGGCCAGCATGGT
Found at i:68162 original size:66 final size:66
Alignment explanation
Indices: 68084--68369 Score: 371
Period size: 66 Copynumber: 4.3 Consensus size: 66
68074 ACCCACGCAG
** * * *
68084 CCAAGTGCTAATCTATATGGCCAGCTTGCT-CAGCCTAGTGCTAACCCATATGACCAAAATGGGC
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TGCAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
68148 AA
65 AA
* *
68150 CCAAGTGGTAATCCTTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATATGGCCAAAATGGGC-
1 CCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
68214 A
66 A
* *
68215 CTCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATACGGCCAAAACGGGC
1 C-CAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
*
68280 AG
65 AA
* * * * *
68282 CCAAGTGCTAATCCCTATGGCCTGCCTGCGTCA-CCCAGTGCTAACTCATATGGCCAAAACGAGC
1 CCAAGTGCTAATCCCTATGGCCAGCCTGTG-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
*
68346 AG
65 AA
*
68348 TCAAGTGCTAATCCCTATGGCC
1 CCAAGTGCTAATCCCTATGGCC
68370 GGCCAACACA
Statistics
Matches: 199, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
65 3 0.02
66 193 0.97
67 3 0.02
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (66 bp):
CCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
A
Found at i:68367 original size:33 final size:32
Alignment explanation
Indices: 68186--68369 Score: 115
Period size: 33 Copynumber: 5.6 Consensus size: 32
68176 TGTGCAGCCC
* *
68186 AGTGCTAACCCATATGGCCAAAATGGGCACTCA
1 AGTGCTAACCC-TATGGCCAAAACGGGCAGTCA
** * * *
68219 AGTGCTAATCCCTATGGCC-AGCCTGTGCAGCCC
1 AGTGCTAA-CCCTATGGCCAAAAC-GGGCAGTCA
* *
68252 AGTGCTAACCCATACGGCCAAAACGGGCAGCCA
1 AGTGCTAACCC-TATGGCCAAAACGGGCAGTCA
** **
68285 AGTGCTAATCCCTATGGCC--TGCCTGC-GTCA
1 AGTGCTAA-CCCTATGGCCAAAACGGGCAGTCA
* *
68315 CCCAGTGCTAACTCATATGGCCAAAACGAGCAGTCA
1 ---AGTGCTAAC-CCTATGGCCAAAACGGGCAGTCA
68351 AGTGCTAATCCCTATGGCC
1 AGTGCTAA-CCCTATGGCC
68370 GGCCAACACA
Statistics
Matches: 114, Mismatches: 24, Indels: 26
0.70 0.15 0.16
Matches are distributed among these distances:
30 3 0.03
31 3 0.03
32 5 0.04
33 87 0.76
34 9 0.08
35 3 0.03
36 4 0.04
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (32 bp):
AGTGCTAACCCTATGGCCAAAACGGGCAGTCA
Found at i:68390 original size:33 final size:33
Alignment explanation
Indices: 68376--68729 Score: 224
Period size: 33 Copynumber: 10.7 Consensus size: 33
68366 GGCCGGCCAA
* * *
68376 CACAACCAAATGCTATTCCTTATGGTCAATCTG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
68409 CACAACCAAATGCTAATCCATATGGTCAACCTG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
** *
68442 CACAACCAAATGCTAATCCATACAGCCAACCTG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* *** * * *
68475 TACAGGTACATGCTAATCTATATGGACAACCTG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* * ****
68508 CTCAGCCAAATGCTAATCCATACAACCAACCTG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* * * ** * * *
68541 CTCAGCCGAATGCTAATCCATACAGCCAGCCTT
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* * ** * *
68574 CACAGCCGAATGCTAATCCATACAGCCAGCCTAG
1 CACAACCAAATGCTAATCCATATGGTCAACCT-G
* * ** * * *
68608 -ACAGCCGAATGCTAATCCATACAGCCAGCCTA
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* ** * *
68640 CACAACCGAATGCTAATCCATACAGCCAGCCTG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* * * *
68673 TACAACCGAATGCTAATCCATATGGCCAACCGG
1 CACAACCAAATGCTAATCCATATGGTCAACCTG
* * *
68706 TACAGCCAAGTGCTAATCCATATG
1 CACAACCAAATGCTAATCCATATG
68730 CCCAACCCAC
Statistics
Matches: 277, Mismatches: 42, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
33 277 1.00
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (33 bp):
CACAACCAAATGCTAATCCATATGGTCAACCTG
Found at i:68423 original size:132 final size:132
Alignment explanation
Indices: 68122--68442 Score: 304
Period size: 132 Copynumber: 2.4 Consensus size: 132
68112 CTCAGCCTAG
* * * ** * * *
68122 TGCTAACCCATATGACCAAAATGGGCAACCAAGTGGTAATCCTTATGGCCAGCCTGTGCAGCCCA
1 TGCTAACCCATACGGCCAAAACGCACAACCAAGTGCTAATCCATATGGCCAGCCTGCGCAGCCCA
* * **** * *
68187 GTGCTAACCCATATGGCCAAAATGGGCACTCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCC
66 GTGCTAACCCATATGGCCAAAACGAGCACTCAAGTGCTAATCCCTATGGCCAGCCAACACAACCA
*
68252 AG
131 AA
** * * *
68254 TGCTAACCCATACGGCCAAAACGGGCAGCCAAGTGCTAATCCCTATGGCCTGCCTGCGTCA-CCC
1 TGCTAACCCATACGGCCAAAACGCACAACCAAGTGCTAATCCATATGGCCAGCCTGCG-CAGCCC
* * *
68318 AGTGCTAACTCATATGGCCAAAACGAGCAGTCAAGTGCTAATCCCTATGGCCGGCCAACACAACC
65 AGTGCTAACCCATATGGCCAAAACGAGCACTCAAGTGCTAATCCCTATGGCCAGCCAACACAACC
68383 AAA
130 AAA
** * * * * * * *
68386 TGCTATTCCTTATGGTC-AATCTGCACAACCAAATGCTAATCCATATGGTCAACCTGC
1 TGCTAACCCATACGGCCAAAAC-GCACAACCAAGTGCTAATCCATATGGCCAGCCTGC
68443 ACAACCAAAT
Statistics
Matches: 153, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
131 3 0.02
132 148 0.97
133 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (132 bp):
TGCTAACCCATACGGCCAAAACGCACAACCAAGTGCTAATCCATATGGCCAGCCTGCGCAGCCCA
GTGCTAACCCATATGGCCAAAACGAGCACTCAAGTGCTAATCCCTATGGCCAGCCAACACAACCA
AA
Found at i:68488 original size:66 final size:65
Alignment explanation
Indices: 68417--68727 Score: 331
Period size: 66 Copynumber: 4.7 Consensus size: 65
68407 TGCACAACCA
* *
68417 AATGCTAATCCATATGGTCAACCTGCACAACCAAATGCTAATCCATACAGCCAACCTGTACAG-G
1 AATGCTAATCCATATGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAACCTGTACAGCG
* * * *
68481 TACATGCTAATCTATATGGACAACCTGCTCAGCCAAATGCTAATCCATACAACCAACCTGCT-CA
1 -A-ATGCTAATCCATATGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAACCTG-TACA
68545 GCCG
63 G-CG
** * * * *
68549 AATGCTAATCCATACAGCCAGCCTTCACAGCCGAATGCTAATCCATACAGCCAGCCTAG-ACAGC
1 AATGCTAATCCATATGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAACCT-GTACAG-
68613 CG
64 CG
** * * * * * *
68615 AATGCTAATCCATACAGCCAGCCTACACAACCGAATGCTAATCCATACAGCCAGCCTGTACAACC
1 AATGCTAATCCATATGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAACCTGTAC-AGC
68680 G
65 G
* * *
68681 AATGCTAATCCATATGGCCAACCGGTACAGCCAAGTGCTAATCCATA
1 AATGCTAATCCATATGGCCAACCTGCACAGCCAAATGCTAATCCATA
68728 TGCCCAACCC
Statistics
Matches: 211, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
65 2 0.01
66 204 0.97
67 4 0.02
68 1 0.00
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.19
Consensus pattern (65 bp):
AATGCTAATCCATATGGCCAACCTGCACAGCCAAATGCTAATCCATACAGCCAACCTGTACAGCG
Found at i:68742 original size:99 final size:99
Alignment explanation
Indices: 68377--68742 Score: 350
Period size: 99 Copynumber: 3.7 Consensus size: 99
68367 GCCGGCCAAC
* * * * * * * *
68377 ACAACCAAATGCTATTCCTTATGGTCAATCT-GCACAACCAAATGCTAATCCATATGGTCAACCT
1 ACAACCGAATGCTAATCCATATGGCCAACCTGGTACAGCCAAATGCTAATCCATAT-GCCAACCT
* * *
68441 GCACAACCAAATGCTAATCCATACAGCCAACCTGT
65 ACACAACCGAATGCTAATCCATACAGCCAGCCTGT
* * * * **
68476 AC-A-GGTACATGCTAATCTATATGGACAACCTGCT-CAGCCAAATGCTAATCCATACAACCAAC
1 ACAACCG-A-ATGCTAATCCATATGGCCAACCTGGTACAGCCAAATGCTAATCCATA-TGCCAAC
* * *
68538 CTGCTCAGCCGAATGCTAATCCATACAGCCAGCCT-T
63 CTACACAACCGAATGCTAATCCATACAGCCAGCCTGT
* ** * * * * *
68574 CACAGCCGAATGCTAATCCATACAGCCAGCCTAG-ACAGCCGAATGCTAATCCATACAGCCAGCC
1 -ACAACCGAATGCTAATCCATATGGCCAACCTGGTACAGCCAAATGCTAATCCATA-TGCCAACC
68638 TACACAACCGAATGCTAATCCATACAGCCAGCCTGT
64 TACACAACCGAATGCTAATCCATACAGCCAGCCTGT
* *
68674 ACAACCGAATGCTAATCCATATGGCCAACC-GGTACAGCCAAGTGCTAATCCATATGCCCAACCC
1 ACAACCGAATGCTAATCCATATGGCCAACCTGGTACAGCCAAATGCTAATCCATATG-CCAACCT
68738 ACACA
65 ACACA
68743 GTCTGTGTCT
Statistics
Matches: 214, Mismatches: 42, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
98 5 0.02
99 206 0.96
100 2 0.01
101 1 0.00
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.19
Consensus pattern (99 bp):
ACAACCGAATGCTAATCCATATGGCCAACCTGGTACAGCCAAATGCTAATCCATATGCCAACCTA
CACAACCGAATGCTAATCCATACAGCCAGCCTGT
Found at i:69565 original size:33 final size:33
Alignment explanation
Indices: 69528--69831 Score: 440
Period size: 33 Copynumber: 9.4 Consensus size: 33
69518 GGGCATGGGA
69528 ATGGGGATGAACAACATGGGCATGAATCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
*
69561 ATGGGGATGAACAACATGGGAATGAATCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
*
69594 ATGGGGATGAACAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
* *
69627 ATGGGGATGAGCAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
*
69660 ATGGGGATG---AACATGGGAATGAATCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
*
69690 ATGGGGATGAACAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
* * *
69723 ATGGGGATGAGCAATATGGGCATGAATCCAGGA
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
* * *
69756 ATGGGGATGAACAACGTGGGCATGAATCGAGGA
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
* *
69789 ATGGGGATG---AACATGAGCATGAACCCAGGC
1 ATGGGGATGAACAACATGGGCATGAATCCAGGC
69819 ATGGGGATGAACA
1 ATGGGGATGAACA
69832 TGGGAATGGG
Statistics
Matches: 246, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
30 53 0.22
33 193 0.78
ACGTcount: A:0.34, C:0.15, G:0.35, T:0.16
Consensus pattern (33 bp):
ATGGGGATGAACAACATGGGCATGAATCCAGGC
Found at i:69683 original size:129 final size:129
Alignment explanation
Indices: 69525--69831 Score: 479
Period size: 129 Copynumber: 2.4 Consensus size: 129
69515 TATGGGCATG
69525 GGAATGGGGATGAACAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGAATGAATCC
1 GGAATGGGGATG---AACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGAATGAATCC
* * *
69590 AGGCATGGGGATGAACAATATGGGCATGAATCCAGGCATGGGGATGAGCAATATGGGCATGAATC
63 AGGCATGGGGATGAACAATATGGGCATGAATCCAGGAATGGGGATGAACAACATGGGCATGAATC
69655 CA
128 CA
* * * *
69657 GGCATGGGGATGAACATGGGAATGAATCCAGGCATGGGGATGAACAATATGGGCATGAATCCAGG
1 GGAATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGAATGAATCCAGG
* * *
69722 CATGGGGATGAGCAATATGGGCATGAATCCAGGAATGGGGATGAACAACGTGGGCATGAATCGA
66 CATGGGGATGAACAATATGGGCATGAATCCAGGAATGGGGATGAACAACATGGGCATGAATCCA
* *
69786 GGAATGGGGATGAACATGAGCATGAACCCAGGCATGGGGATGAACA
1 GGAATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACA
69832 TGGGAATGGG
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
129 150 0.93
132 11 0.07
ACGTcount: A:0.34, C:0.15, G:0.36, T:0.16
Consensus pattern (129 bp):
GGAATGGGGATGAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGAATGAATCCAGG
CATGGGGATGAACAATATGGGCATGAATCCAGGAATGGGGATGAACAACATGGGCATGAATCCA
Found at i:69709 original size:96 final size:96
Alignment explanation
Indices: 69528--69828 Score: 455
Period size: 96 Copynumber: 3.1 Consensus size: 96
69518 GGGCATGGGA
* *
69528 ATGGGGATGAACAACATGGGCATGAATCCAGGCATGGGGATGAACAACATGGGAATGAATCCAGG
1 ATGGGGATGAGCAATATGGGCATGAATCCAGGCATGGGGATG---AACATGGGAATGAATCCAGG
69593 CATGGGGATGAACAATATGGGCATGAATCCAGGC
63 CATGGGGATGAACAATATGGGCATGAATCCAGGC
69627 ATGGGGATGAGCAATATGGGCATGAATCCAGGCATGGGGATGAACATGGGAATGAATCCAGGCAT
1 ATGGGGATGAGCAATATGGGCATGAATCCAGGCATGGGGATGAACATGGGAATGAATCCAGGCAT
69692 GGGGATGAACAATATGGGCATGAATCCAGGC
66 GGGGATGAACAATATGGGCATGAATCCAGGC
* * *
69723 ATGGGGATGAGCAATATGGGCATGAATCCAGGAATGGGGATGAACAACGTGGGCATGAATCGAGG
1 ATGGGGATGAGCAATATGGGCATGAATCCAGGCATGGGGATGAAC-A--TGGGAATGAATCCAGG
* * *
69788 AATGGGGATGAAC---ATGAGCATGAACCCAGGC
63 CATGGGGATGAACAATATGGGCATGAATCCAGGC
69819 ATGGGGATGA
1 ATGGGGATGA
69829 ACATGGGAAT
Statistics
Matches: 191, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
96 124 0.65
97 1 0.01
99 66 0.35
ACGTcount: A:0.33, C:0.15, G:0.36, T:0.17
Consensus pattern (96 bp):
ATGGGGATGAGCAATATGGGCATGAATCCAGGCATGGGGATGAACATGGGAATGAATCCAGGCAT
GGGGATGAACAATATGGGCATGAATCCAGGC
Found at i:69798 original size:18 final size:18
Alignment explanation
Indices: 69738--69799 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
69728 GATGAGCAAT
*
69738 ATGGGCATGAATCCAGGA
1 ATGGGCATGAATCAAGGA
* *
69756 ATGGGGATGAA-CAACG-
1 ATGGGCATGAATCAAGGA
*
69772 -TGGGCATGAATCGAGGA
1 ATGGGCATGAATCAAGGA
*
69789 ATGGGGATGAA
1 ATGGGCATGAA
69800 CATGAGCATG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.26
16 3 0.09
17 3 0.09
18 19 0.56
ACGTcount: A:0.34, C:0.11, G:0.39, T:0.16
Consensus pattern (18 bp):
ATGGGCATGAATCAAGGA
Found at i:74002 original size:2 final size:2
Alignment explanation
Indices: 73991--74027 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
73981 AATATTAGAT
*
73991 TA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74028 TATTTAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:74832 original size:3 final size:3
Alignment explanation
Indices: 74780--74822 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
74770 CAATGTTTTA
* * *
74780 AAT AAT AAAT TAT AAT AAT GAT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
74823 GTGATAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:76991 original size:20 final size:20
Alignment explanation
Indices: 76954--76994 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
76944 TTAAAATACA
* *
76954 TATAATTATTCATCTAATAT
1 TATAACTATTCAACTAATAT
*
76974 TATAACTATTCAAGTAATAT
1 TATAACTATTCAACTAATAT
76994 T
1 T
76995 GTTTGAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAACTATTCAACTAATAT
Found at i:77952 original size:27 final size:26
Alignment explanation
Indices: 77922--78021 Score: 69
Period size: 27 Copynumber: 3.7 Consensus size: 26
77912 TGATTTTTAG
77922 TTTTGAAGGGGCCCAAAAAATTTTAAC
1 TTTT-AAGGGGCCCAAAAAATTTTAAC
* *** *
77949 TTTTAA-AGGTAAAAAAAATTTACCAAC
1 TTTTAAGGGGCCCAAAAAATTT--TAAC
*
77976 TTTTAAGGGGTCCCAAAAAATTTTTTTAGC
1 TTTTAAGGGG-CCCAAAAAA---TTTTAAC
78006 TTTTAAGGGG-CCAAAA
1 TTTTAAGGGGCCCAAAA
78022 TTGTTTTTAC
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
25 11 0.20
26 2 0.04
27 13 0.24
28 8 0.15
29 6 0.11
30 12 0.22
32 3 0.05
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (26 bp):
TTTTAAGGGGCCCAAAAAATTTTAAC
Found at i:82948 original size:315 final size:315
Alignment explanation
Indices: 82360--82988 Score: 1012
Period size: 315 Copynumber: 2.0 Consensus size: 315
82350 TTGTTTTTTC
*
82360 TCTGGGTAGCCAGATGGAATTACGGGGAGTTTCACATAATGCTTATTCTTTCACTATCTTGATTA
1 TCTGGGTAGCCAGATGGAACTACGGGGAGTTTCACATAATGCTTATTCTTTCACTATCTTGATTA
*
82425 ATTGCTTTTGTCAGTTAGGTAAAGTTGATTTTGGGTTTTCTGTTTTGGGGAAAATGCTCAAGTTA
66 ATTGCTTTTGTCAGTTAGATAAAGTTGATTTTGGGTTTTCTGTTTTGGGGAAAATGCTCAAGTTA
* *
82490 GGTTTTGAACCTACTGTCGTGACTTTGTCCACTTTGATTAATGGACTTTGTAATCAAAGCAGAGT
131 GGATTTGAACCTACTGTCGTAACTTTGTCCACTTTGATTAATGGACTTTGTAATCAAAGCAGAGT
** * * *
82555 TTCTCAGGCTGTGAGTTTGTTTTACGAAATGATCGAAAAAGGGTATCGACCTGATTCATTTGCTT
196 TTCTCAGGCTGCAAGTTTGTTTGACGAAATGATCGAAAAAGGGTATCAACCTGATTCAGTTGCTT
* *
82620 GCAATAGAGTACTTAATGGGTTGTGTAAGACTGGGAACACTGGTCGAGCTGTTAT
261 ACAATACAGTACTTAATGGGTTGTGTAAGACTGGGAACACTGGTCGAGCTGTTAT
* *
82675 TCTGGGTAGCCAGATGGAACTATGGGGAGTTTCACATGATGCTTATTCTTTCAAC-ATCTTGATT
1 TCTGGGTAGCCAGATGGAACTACGGGGAGTTTCACATAATGCTTATTCTTTC-ACTATCTTGATT
82739 AATTGCTTTTGTCAGTTAGATAAAGTTGATTTTGGGTTTTCTGTTTTGGGGAAAATGCTCAAGTT
65 AATTGCTTTTGTCAGTTAGATAAAGTTGATTTTGGGTTTTCTGTTTTGGGGAAAATGCTCAAGTT
*
82804 AGGATTTGAACCTGA-TGTTGTAACTTTGTCCACTTTGATTAATGGACTTTGTAATCAAAGCA-A
130 AGGATTTGAACCT-ACTGTCGTAACTTTGTCCACTTTGATTAATGGACTTTGTAATCAAAGCAGA
* * * * *
82867 GCTTTCTCAGGCTGCAATTTTGTTTGATGAGATGATTGAAAAAGGGTATCAACCTGATTTAGTTG
194 G-TTTCTCAGGCTGCAAGTTTGTTTGACGAAATGATCGAAAAAGGGTATCAACCTGATTCAGTTG
* **
82932 CTTACAATACAGTACTTAATGGTTTGTGTAAGGTTGGGAACACTGGTCGAGCTGTTA
258 CTTACAATACAGTACTTAATGGGTTGTGTAAGACTGGGAACACTGGTCGAGCTGTTA
82989 GATTTCTAAG
Statistics
Matches: 289, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
314 2 0.01
315 284 0.98
316 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (315 bp):
TCTGGGTAGCCAGATGGAACTACGGGGAGTTTCACATAATGCTTATTCTTTCACTATCTTGATTA
ATTGCTTTTGTCAGTTAGATAAAGTTGATTTTGGGTTTTCTGTTTTGGGGAAAATGCTCAAGTTA
GGATTTGAACCTACTGTCGTAACTTTGTCCACTTTGATTAATGGACTTTGTAATCAAAGCAGAGT
TTCTCAGGCTGCAAGTTTGTTTGACGAAATGATCGAAAAAGGGTATCAACCTGATTCAGTTGCTT
ACAATACAGTACTTAATGGGTTGTGTAAGACTGGGAACACTGGTCGAGCTGTTAT
Found at i:83425 original size:105 final size:104
Alignment explanation
Indices: 83316--83679 Score: 383
Period size: 105 Copynumber: 3.5 Consensus size: 104
83306 TTCTTTAATG
* * *
83316 CAATGAGAAAGCAAGGCGTCAAGCCTGATGTTGTCA-GCTATAATATATTGGTTGATGCATATTG
1 CAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACG-TATAATATATTGGTTGATGCGTATTG
* * * * *
83380 TAAGGAGAGGCTAATTTCTGAATCTTTGGATATAGTTCACA
65 CAAGGAGAGGAT-ATTTCTGAAGCTGTAGATATAGTTCACA
* * * * *
83421 CAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACGTATAGTACATTGGTTGATGTGCATTGC
1 CAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACGTATAATATATTGGTTGATGCGTATTGC
* ** * * * * *
83486 AAGGAGGGGAGGGTTTCTGAAGCCGAAGATATTGTTGATA
66 AAGGAGAGGA-TATTTCTGAAGCTGTAGATATAGTTCACA
* * *
83526 GAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGC
1 CAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACGTATAATATATTGGTTGATGCGTATTGC
* *
83591 AAGGAGAGGAGTATTTCTAAAGCTGTAGATACCA-TTGC-CA
66 AAGGAGAGGA-TATTTCTGAAGCTGTAGATA-TAGTT-CACA
* ** *
83631 GAATGAGAAAGCAAGGTGTGAAGCCTGATGTTGTCACGTATAATATATT
1 CAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACGTATAATATATT
83680 TATCGATGCA
Statistics
Matches: 213, Mismatches: 42, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
105 212 1.00
106 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (104 bp):
CAATGAGAAAGCAAGGCATTAAGCCTGATGTTGTCACGTATAATATATTGGTTGATGCGTATTGC
AAGGAGAGGATATTTCTGAAGCTGTAGATATAGTTCACA
Found at i:83713 original size:210 final size:209
Alignment explanation
Indices: 83316--83761 Score: 485
Period size: 210 Copynumber: 2.1 Consensus size: 209
83306 TTCTTTAATG
* ** *
83316 CAATGAGAAAGCAAGGCGTCAAGCCTGATGTTGTCAGCTATAATATATTGGTTGATGCATATTGT
1 CAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAGCTATAATATATTGGTTGATGCATATTGC
* * * * *
83381 AAGGAGAGGCTAATTTCTGAATCTTTGGATATAGTTCACACAATGAGAAAGCAAGGCATTGAGCC
66 AAGGAGAGGCTAATTTCTAAAGCTGTAGATACAGTTCACACAATGAGAAAGCAAGG-ATTGAGCC
* * * **
83446 TGATGTTGTCACGTATAGTACATTGGTTGATGTGCATTGCAAGGAGGGGAGGGTTTCTGAAGCCG
130 TGATGTTGTCACGTATAATACATTGATCGATGCACATTGCAAGGAGGGGAGGGTTTCTGAAGCCG
* *
83511 AA-GATATTGTTGATA
195 AATG-TATTGTCGACA
* * *
83526 GAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTGA-CGTATAATATATTGGTTGATGCGTATTG
1 CAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAGC-TATAATATATTGGTTGATGCATATTG
* *
83590 CAAGGAGAGGAGT-ATTTCTAAAGCTGTAGATACCA-TTGC-CAGAATGAGAAAGCAAGG-TGTG
65 CAAGGAGAGG-CTAATTTCTAAAGCTGTAGATA-CAGTT-CACACAATGAGAAAGCAAGGAT-TG
* * * * * *
83651 AAGCCTGATGTTGTCACGTATAATATATTTATCGATGCACTTTG-TAGGAATGGGATGGTTTCTG
126 -AGCCTGATGTTGTCACGTATAATACATTGATCGATGCACATTGCAAGG-AGGGGAGGGTTTCTG
*
83715 AAGCTGAATGTATTGTCGACA
189 AAGCCGAATGTATTGTCGACA
*
83736 CAATGAGAAAAG-AATGCATTGAGCCT
1 CAATGAG-AAAGCAAGGCATTGAGCCT
83762 AATTTTGTTA
Statistics
Matches: 197, Mismatches: 30, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
208 1 0.01
209 6 0.03
210 182 0.92
211 8 0.04
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (209 bp):
CAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAGCTATAATATATTGGTTGATGCATATTGC
AAGGAGAGGCTAATTTCTAAAGCTGTAGATACAGTTCACACAATGAGAAAGCAAGGATTGAGCCT
GATGTTGTCACGTATAATACATTGATCGATGCACATTGCAAGGAGGGGAGGGTTTCTGAAGCCGA
ATGTATTGTCGACA
Found at i:86996 original size:16 final size:17
Alignment explanation
Indices: 86975--87008 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
86965 ATAGAATATT
*
86975 ATTTTATTAATT-TAAA
1 ATTTTATAAATTATAAA
86991 ATTTTATAAATTATAAA
1 ATTTTATAAATTATAAA
87008 A
1 A
87009 AATAATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTATAAATTATAAA
Found at i:89526 original size:105 final size:105
Alignment explanation
Indices: 89373--89684 Score: 428
Period size: 105 Copynumber: 3.0 Consensus size: 105
89363 ATATTTTCAT
* * * * *** *
89373 GTATAATATGTTGATTGATGCACATTGCAAGGAGGGGACAATTTCTGAAGCTGTAGATATTGTTG
1 GTATAGTATATTGGTTGATGCACATTGCAAGGAAGGGATGGTTTCTGAAGCTGAAGATATTGTTG
*
89438 ACACAATGAGAAAGCAAGGGATTGAGCCTAATGTTGTCAC
66 ACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCAC
* * * *
89478 GTATAGTATATTGGTTGATGCGCATTGCAAGGAAGGGATGGTTCCTGAAGCTAAACATATTGTTG
1 GTATAGTATATTGGTTGATGCACATTGCAAGGAAGGGATGGTTTCTGAAGCTGAAGATATTGTTG
* *
89543 AGACAATGATAAAGCAAGGCATTGAGCCTAATGTTGTCAC
66 ACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCAC
* * *
89583 GTATAGTATATTGGTCGATGCACTTTGCAA-GAAGGGGATGGTTTTTGAAGCTGAAGATATTGTT
1 GTATAGTATATTGGTTGATGCACATTGCAAGGAA-GGGATGGTTTCTGAAGCTGAAGATATTGTT
* *
89647 GACACAATGAGAAATCAAGGCATTGAGCCTGATGTTGT
65 GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGT
89685 TACCTATAAC
Statistics
Matches: 180, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
104 3 0.02
105 177 0.98
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (105 bp):
GTATAGTATATTGGTTGATGCACATTGCAAGGAAGGGATGGTTTCTGAAGCTGAAGATATTGTTG
ACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCAC
Done.